He made London his home in 1559 and very successfully resumed his practice as a doctor, soon becoming house physician at St. Bartholomew's Hospital. Despite racial prejudice and professional jealousy, he developed a large practice among powerful people including Robert Dudley and Francis Walsingham. Rumor held that his success was less due to his medical skill and more to his skill at flattery and self-promotion. In a 1584 libelous pamphlet attacking Dudley, it was suggested that Lopez distilled poisons for Dudley and other nobleman as well. In 1586, he reached the pinnacle of his profession; he was made physician-in-chief to Queen Elizabeth. Lopez was held in the queen's favour for, in 1589, she granted him a monopoly on the importation of aniseed and sumac into England. His success continued as he neared retirement. He was viewed, at least outwardly, as being a dutiful practicing Protestant.

In October of 1593, he was wealthy and generally respected. At that time, he owned a house in Holborn and had a son enrolled at Winchester College. However, also in October, a complex web of conspiracy against Dom António began to come to light. Subsequently, Lopez was accused by Robert Devereux of conspiring with Spanish emissaries to poison the Queen. He was arrested on January 11594, convicted in February, and subsequently executed (hanged, drawn and quartered) on June 7. The Queen herself was uncertain of his guilt (hence the delay in his execution) and he maintained his innocence of treason and his being converted from Judaism to Christianity until his execution. According to William Camden, right before he was hanged he said to the crowd that he loved his queen as well as he loved Jesus Christ; the crowd laughed at this statement, taking it for a thinly veiled confession, as in their eyes he was still a Jew.